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Answer: Error in cnetplot
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Guido Hooiveld
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4.1k
Unfortunately you did not show how you generated your input data (object enrichment), nor did you show the output from `sessionInfo()`.
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Answer: getBM from biomaRt inconsistencies found with .gtf files across multiple species
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Mike Smith
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I think this is because Ensembl can assign different Gene IDs to "the same gene" if it is found both on a standard chromosome and a scaffol…
Comment: Explannation for ROAST results
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Jay
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Yes! Tnx for your reply. I didn't notice the group design problem, so stupid. Thank you!
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ATpoint
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The `contrast = 2` in an intercept-less design test whether the expression in the 2nd group is not 0. You can easily solve this by using `~…
Comment: Explannation for ROAST results
by
Jay
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BTW, AP1 is a character, composed of gene entrez ID, so is HIF1, UPR, etc al. And the rownames of `expr.i` is also gene entrez ID.
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